Lautenschlager, Ulrich and Scheunert, Agnes (2023) LoCoLotive: In silico mining for low-copy nuclear loci based on target capture probe sets and arbitrary reference genomes. APPLICATIONS IN PLANT SCIENCES, 11 (6). e11535. ISSN 2168-0450
Full text not available from this repository. (Request a copy)Abstract
PremiseUniversal target enrichment probe kits are used to circumvent the individual identification of loci suitable for phylogenetic studies in a given taxon. Under certain circumstances, however, target capture can be inefficient and costly, and lower numbers of marker loci may be sufficient. We therefore propose a computational pipeline that enables the easy identification of a subset of promising candidate loci for a taxon of interest. Methods and ResultsTarget sequences used for probe design are filtered based on an assembled reference genome, resulting in presumably intron-containing single-copy loci as present in the reference taxon. The applicability of the proposed approach is demonstrated based on two probe kits (universal and family-specific) in combination with several publicly available reference genomes. ConclusionsGuided by commercial probe kits, LoCoLotive enables fast and cost-efficient marker mining. Its accuracy mainly depends on the quality of the reference genome and its relatedness to the taxa under study.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | SPECIES NETWORKS; PERFORMANCE; PROGRESS; MAFFT; low-copy loci; marker mining; nuclear marker; probe kit; single-copy loci; target capture; target enrichment |
| Subjects: | 500 Science > 580 Botanical sciences |
| Divisions: | Biology, Preclinical Medicine > Institut für Pflanzenwissenschaften > Group Plant Systematics and Evolution (Prof. Dr. Christoph Oberprieler) |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 13 Mar 2024 10:04 |
| Last Modified: | 13 Mar 2024 10:04 |
| URI: | https://pred.uni-regensburg.de/id/eprint/59548 |
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